Different approaches toward an automatic structural alignment of drug molecules: Applications to sterol mimics,thrombin and thermolysin inhibitors

Summary A relative comparison of the binding properties of different drug molecules requires their mutual superposition with respect to various alignment criteria. In order to validate the results of different alignment methods, the crystallographically observed binding geometries of ligands in the pocket of a common protein receptor have been used. The alignment function in the program SEAL that calculates the mutual superposition of molecules has been optimized with respect to these references. Across the reference data set, alignments could be produced that show mean rms deviations of approximately 1 Å compared to the experimental situation. For structures with obvious skeletal similarities a multiple-flexible fit, linking common pharmacophoric groups by virtual springs, has been incorporated into the molecular mechanics program MOMO. In order to combine conformational searching with comparative alignments, the optimized SEAL approach has been applied to sets of conformers generated by MIMUMBA, a program for conformational analysis. Multiple-flexible fits have been calculated for inhibitors of ergosterol biosynthesis. Sets of different thrombin and thermolysin inhibitors have been conformationally analyzed and subsequently aligned by a combined MIMUMBA/SEAL approach. Since for these examples crystallographic data on their mutual alignment are available, an objective assessment of the computed results could be performed. Among the generated conformers, one geometry could be selected for the thrombin and thermolysin inhibitors that approached reasonably well the experimentally observed alignment.     

Isoperichoric focusing field-flow fractionation and thin layer isoperichoric focusing based on coupling of gradient generated by primary field with secondary field action: general principles and performances

The primary field forces can generate spatially oriented gradient of the effective property of a continuum or pseudo-continuum fluid (carrier liquid). When this gradient is coupled with the action of a secondary field of identical or different nature the isoperichoric focused zones of the dispersed species can appear. Consequently, they can be separated according to differences responding to the property gradient of the carrier liquid. This concept can be applied under static (non-flow) conditions in thin layer focusing as well as under dynamic conditions with the elution due to the carrier liquid flow in focusing field-flow fractionation. The gradient established by the action of the primary field and the concentration distribution of the isoperichoric focused zone formed by the coupled effect of the gradient and of the primary or secondary field are described theoretically. The rigorous relationship describing the shape of the focused zone is compared with the approximate solutions. The performances of the proposed principle were evaluated by model calculations. Potential experimental configurations considering the implementation of the static and dynamic conditions are discussed. The generalized isoperichoric focusing theory can be applied to describe the particular processes operating in analytical and preparative focusing separations of the particles of various, but especially of biological origin.     

Synthese und Kristallstrukturen der Phosphanimin-Komplexe MCl2(Me3SiNPMe3)2 mit M = Zn und Co,und CoCl2(HNPMe3)2

Syntheses and Crystal Structures of the Phosphaneimine Complexes MCl₂(Me₃SiNPMe₃)₂ with M = Zn and Co, and CoCl₂(HNPMe₃)₂ The molecular complexes MCl₂(Me₃SiNPMe₃)₂ (M = Zn, Co) have been prepared by the reaction of the dichlorides of zinc and cobalt with Me₃SiNPMe₃ in CH₃CN and CH₂Cl₂, respectively, whereas the complex CoCl₂(HNPMe₃)₂ has been prepared by the reaction of CoCl₂ with NaF in boiling acetonitrile in the presence of Me₃SiNPMe₃. All complexes were characterized by IR spectroscopy and by crystal structure determinations. The complexes MCl₂(Me₃SiNPMe₃)₂ crystallize isotypically. ZnCl₂(Me₃SiNPMe₃)₂: Space group P2₁2₁2₁, Z = 4, 2677 observed unique reflections, R = 0.024. Lattice dimensions at ?70°C: a = 1243.6; b = 1319.0; c = 1464.7 pm. CoCl₂(Me₃SiNPMe₃)₂: Space group P2₁2₁2₁, Z = 4, 3963 observed unique reflections, R = 0,071. Lattice dimensions at ?80°C: a = 1236.3; b = 1317.4; c = 1457.6 pm. CoCl₂(HNPMe₃)₂ · CH₂Cl₂: Space group Pbca, Z = 8, 1354 observed unique reflections, R = 0.055. Lattice dimensions at ?80°C: a = 1247.3; b = 998.4; c = 2882.4 pm. All complexes have monomeric molecular structures, in which the metal atoms are coordinated in a distorted tetrahedral fashion by the two chlorine atoms and by the nitrogen atoms of the phosphaneimine molecules.     

Spectral and Thermal Studies of Rare Earth Element 3-methylglutarates

Conditions for the formation of rare earth element (Y, La–Lu) 3-methylglutarates were studied and their quantitative composition and solubilities in water at 293 K were determined (10^–2 mol dm^–3). The IR spectra of the prepared complexes with general formula Ln₂(C₆H₈O₄)₃ nH₂O (n=3–8) were recorded and their thermal decomposition in the air were investigated. During heating the hydrated 3-methylglutarates are dehydrated in one step and next anhydrous complexes decompose to oxides Ln₂O₃ with intermediate formation Ln₂O₂CO₃ (Y, La, Nd–Gd) or directly to the oxides, Ln₂O₃, CeO₂, Pr₆O₁₁ and Tb₄O₇ (Ce, Pr, Tb–Lu). This revised version was published online in August 2006 with corrections to the Cover Date.     

Spectral regions selection to improve prediction ability of PLS models by changeable size moving window partial least squares and searching combination moving window partial least squares

Changeable size moving window partial least squares (CSMWPLS) and searching combination moving window partial least squares (SCMWPLS) are proposed to search for an optimized spectral interval and an optimized combination of spectral regions from informative regions obtained by a previously proposed spectral interval selection method, moving window partial least squares (MWPLSR) [Anal. Chem. 74 (2002) 3555]. The utilization of informative regions aims to construct better PLS models than those based on the whole spectral points. The purpose of CSMWPLS and SCMWPLS is to optimize the informative regions and their combination to further improve the prediction ability of the PLS models. The results of their application to an open-path (OP)/FT-IR spectra data set show that the proposed methods, especially SCMWPLS can find out an optimized combination, with which one can improve, often significantly, the performance of the corresponding PLS model, in terms of low prediction error, root mean square error of prediction (RMSEP) with the reasonable latent variable (LVs) number, comparing with the results obtained using whole spectra or direct combination of informative regions for a compound. Regions consisting of the combinations obtained can easily be explained by the existence of IR absorption bands in those spectral regions.     

Efficient oxidative dimerization of 1-naphthols to 2,2-binaphthyls with dioxygen mediated by semiconductors

A novel and efficient oxidative dimerization of 1-naphthols 1 with dioxygen in the presence of several semiconductors including SnO₂, ZrO₂, and activated charcoal as catalytic mediators took place selectively to give the corresponding 2,2^′-binaphthols 2 or 2,2^′-binaphthyl-1,1^′-quinones 3 in excellent yields without light irradiation. Among these semiconductors, the catalytic activity of SnO₂ could be fully restored by appropriate reactivation treatment after oxidation. The products 2 and 3 should be useful as synthetic intermediates for natural binaphthyls.     

Carbon dioxide reduction under visible light: a comparison of cadmium sulfide and titania photocatalysts

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A Green's function approach to the photoelectron spectrum of bis(π-allyl)nickel[1]

The vertical ionization potentials of bis(-allyl)nickel (see (1) in Fig. 1) are calculated by means of the Green's function approach within a semiempirical INDO extension to the first transition metal series. The computed ionization potentials are in good agreement with an experimentally deduced assignment. In contrast to earlier theoretical and experimental studies, the 7a _u () level is predicted on top of the levels corresponding to the Ni 3d orbitals. Our approach leads to a complete assignment of the PE spectrum of (1) in the outer valence region.     

Borchelate und Bormetallchelate, 4. Mitt.

The i.r., u. v.,¹H n.m.r.,¹³C n.m.r., and¹¹B n.m.r. spectra of several substituted diphenylboron chelates derived from salicylaldehyde azomethines were compared with respect to the influence of the amine substituentR. O–B–N-6-ring constitution of the chelates29–32 [R=OH, NH₂, NHC₆H₅, N(CH₃)₂] can be deduced from the spectra.

Als 3. Mitt. gilt:F. Umland undE. Hohaus mit Beiträgen vonW. Riepe, K. Brodte, C. Schleyerbach undD. Szonn. Untersuchungen über borhaltige Ringsysteme vom Chelattyp. Forschungsbericht des Landes Nordrhein-Westfalen Nr. 2538. Opladen: Westdeutscher Verlag. 1976.     

Determination of phenol and catechol concentrations with oxygen probes coated with immobilized enzymes or immobilized cells

The enzyme phenol 2-hydroxylase was immobilized on Sepharose and used in conjunction with an O₂ electrode for quantitating phenol. Similarly, catechol 1,2-oxygenase was used for quantitating catechol. A third probe was prepared by immobilization ofTrichosporon cutaneum cells rather than purified phenol 2-hydroxylase for phenol quantitation. The whole cell system gave results comparable to the immobilized enzyme system.